We are pleased to introduce version 11.1 of our ChemDoodle 2D software. This update is free for all ChemDoodle subscriptions, Lifetime and Site licenses. Licenses are as little as $19, and we have a free trial available at: https://www.chemdoodle.com/

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Executive Summary

ChemDoodle 2D v11.1 is a feature and stability update and is recommended for all users. The major new feature is advanced repeat unit support, both in graphical drawing and cheminformatics interpretation and expansion. Other notable features include improved reaction building interfaces and feedback, arc-length controls, and smaller EPS file output. This update also corrects an issue introduced by macOS 10.15.6, leading to corrupted and missing windows. So if you are experiencing these issues, make sure to install this update.

Additions

  1. Full and advanced repeat unit support. You may now easily draw brackets with repeating unit values; see section 9.14 of the ChemDoodle 2D User Guide. You may place in any text you desire, but 0 and positive integers will be recognized by the cheminformatics engine in ChemDoodle 2D and will be expanded accordingly; see section 13.13. Repeat units can be adjacent and fully embedded. You may also expand repeat units to their all atom models. Errors in repeat unit drawing (for instance if you draw a repeat unit between bonds in two separate molecules) will be shown by the warning system in ChemDoodle 2D; see section 13.5.
  2. The reaction editor has been improved, making it easier to see what your actions are doing and how molecules will participate in the reaction. If you hover molecules in the reaction editor, the molecule in the document will now be highlighted. Centering of reaction text in the editor is now the default. If you have defined a selection of molecules when you edit a reaction, only those molecules (and any molecules already assigned to the reaction) will be present in the reaction editor.
  3. Hovering over a reaction now visually describes its interpretation. Reactants will be highlighted in a cyan color while products are highlighted in a magenta color.
  4. You can now control the arc-length of an arc or curved arrow by using the two new control points that flank the endpoints of the arc using a selection tool or any arc tool.
  5. Made adding attributes a little quicker by automatically choosing the last attribute name, and updating the list order when a previous name is selected and used.
  6. EPS shortcuts have been implemented for smaller EPS image files.
  7. You can now paste IUPAC name text directly as a chemical structure by using the Edit>Paste Text as Chemical>IUPAC Name menu item, also found in the right-click menu.
  8. Both the menu item for generating an IUPAC name and the auto-updating label for IUPAC names will display more relevant error information when an IUPAC name cannot be generated.

Fixes

  1. macOS 10.15.6 exposed a bug in Java, causing some windows to be corrupted or not appear. This may prevent users from saving new files or opening windows such as the Preferences window. This update corrects this issue.
  2. Fixed issue where highlighted text in the reaction editor would result in highlighted text in the document.
  3. Fixed issue with stereochemistry where the depth search picked the highest priority difference, not the closest difference; this mainly affected centers in evenly sized symmetrical rings, where a heteroatom is opposite the center.
  4. SMARTS now properly catches lowercase "p" for aromatic phosphorus.
  5. Transform statistics are now shown when editing shapes using shape tools.
  6. Corrected issue where editing a shape using a shape tool would incorrectly move any current selection.
  7. Corrected issue of rare artifacts in EMF output, mainly in spectra and arrowheads.
  8. Corrected issue where tables were not properly output to several vector image formats.
  9. The quick-start guide will now be placed in a scroll pane if the screen height is not suitable. Some Windows users will small screens or increased resolution were not able to close the quick-start window easily.
  10. Corrected issue where the workspace could corrupt if an external monitor where ChemDoodle 2D was being displayed was disconnected.
  11. Minor text corrections.